Can someone please explain the concept of ScarHRD?
HRD=The unweighted sum of LOH+LST+TAI
How are these scores calculated?
According to the original publication:
A sample’s LOH score is the total number of LOH regions across the entire genome that are larger than 15 Mb but do not cover whole chromosomes.
The LST is defined as a chromosomal break between adjacent regions of at least 10 Mb, with a distance between them not larger than 3 Mb.
The number of telomeric allelic imbalances is the number of AIs (the unequal contribution of parental allele sequences with or without changes in the overall copy number of the region) that extend to the telomeric end of a chromosome.
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version 2.3.6
How are these scores help in HRD? Do they sum all of these scores? When i tried doing it for our in-house sampe i didn't arrive at >=42 but values less than that of 36. Please help! Also the tool ScarHRD performs run only till chr7. Can anyone suggest alternatives or solution?
As you mention in the original question, the score is the sum.
Why do you expect >=42?
You should try posting this issue on their GitHub with more information about the exact error you are getting.